Import coyote data

Functions

Load genetic data into coyote. This can be achieved in two ways.

• Using flags via the load command. This is similar to the legacy perl-script
• Using YAML-file via the yaml command.

This new CLI is written in python and combines all various data types that 4 different perl-scripts handled before. It also handles both DNA and RNA samples. Additionally improved case_id incrementation that was crudely handled by perl-scripts before and adds the option to update cases with new information or overwriting old information. This could be both meta-information or types of genetic variation.

Handles data types:

• CSV (gzipped)
• YAML
• JSON
• VCF

import_coyote_sample.py --help

import_coyote_sample.py load --help

import_coyote_sample.py yaml --help

todo

• make sure update flag works for yaml import
• documentation
• better testing examples
  • (SNV-indels that are not all filtered)
  • fewer of other data types
• create pip requirements.txt